Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F50 I1 R1 170 39.5 1266514 99.2% 1256381 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,053,097 A→G V89A (GTA→GCA)  yccM ← putative 4Fe‑4S membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,053,0970AG95.0% 137.8 / ‑1.2 40V89A (GTA→GCA) yccMputative 4Fe‑4S membrane protein
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (23/15);  total (24/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GTTTGTTACCGAGATCGCCGATTAATTCAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTACAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATAAATATT  >  NC_000913/1052948‑1053236
                                                                                                                                                     |                                                                                                                                           
gTTTGTTACCGAGATCGCCGATTAATTCAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTAc                                                                                                                                            <  1:595202/151‑1 (MQ=255)
  ttGTTACCGAGATCGCCGATTAATTCAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCa                                                                                                                                           >  2:361693/1‑150 (MQ=255)
       aCCGAGATCGCCGATTAATTCAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCt                                                                                                                                      >  2:423283/1‑150 (MQ=255)
                           cAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGccc                                                                                                                 >  2:466742/1‑151 (MQ=255)
                              aaaGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGc                                                                                                              >  1:592508/1‑151 (MQ=255)
                               aaGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGc                                                                                                              >  1:601806/1‑150 (MQ=255)
                                 gCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAAt                                                                                                           <  1:257483/151‑1 (MQ=255)
                                   gTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCg                                                                                                         >  2:255720/1‑151 (MQ=255)
                                       cAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGt                                                                                                       >  1:232249/1‑149 (MQ=255)
                                        aaCCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTagc                                                                                                    >  2:179915/1‑151 (MQ=255)
                                        aaCCGGGCATAACCATGAGCAAAAAGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTagc                                                                                                    >  1:147934/1‑151 (MQ=255)
                                           cGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTagcc                                                                                                   >  1:41241/1‑149 (MQ=255)
                                               cATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCtt                                                                                             >  1:514300/1‑151 (MQ=255)
                                                 tAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCg                                                                                           >  2:307449/1‑151 (MQ=255)
                                                   aCCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGAt                                                                                         <  1:576587/151‑1 (MQ=255)
                                                         aGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTcc                                                                                   >  2:141415/1‑151 (MQ=255)
                                                          gCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTagcca                                                                                                  <  1:251590/135‑1 (MQ=255)
                                                          gCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTagcca                                                                                                  >  2:251583/1‑135 (MQ=255)
                                                               aGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCt                                                                             >  2:485365/1‑151 (MQ=255)
                                                                      tttGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGAc                                                                       <  2:609396/150‑1 (MQ=255)
                                                                          aGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATg                                                                  <  2:57946/151‑1 (MQ=255)
                                                                           gTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGt                                                                 <  1:615121/151‑1 (MQ=255)
                                                                             aaTAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCg                                                               >  1:404960/1‑151 (MQ=255)
                                                                                 gACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCt                                                           >  2:429253/1‑151 (MQ=255)
                                                                                  aCTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCt                                                           >  1:138698/1‑150 (MQ=255)
                                                                                  aCTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCt                                                           >  2:34540/1‑150 (MQ=255)
                                                                                                  gCGGCCAATACCAGCAGCGCAGTGGCGTGGAGGGACGGTATCTGACCTGATGCAAAAATATATATCAGGTTCTTCAGTACGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGaaa                                           <  2:9787/150‑1 (MQ=255)
                                                                                                    gACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAAt                                          >  2:89980/1‑149 (MQ=255)
                                                                                                    gACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAg                                        <  2:486259/151‑1 (MQ=255)
                                                                                                    gACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTACAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAAt                                          >  2:42524/1‑149 (MQ=255)
                                                                                                        aaTAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCa                                    <  2:432195/151‑1 (MQ=255)
                                                                                                                cATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATAc                            >  2:484931/1‑151 (MQ=255)
                                                                                                                   cgcgGCGGCGTGGACGGACGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAg                         <  1:255727/151‑1 (MQ=255)
                                                                                                                              ggacggacGGTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATgg               <  2:162691/150‑1 (MQ=255)
                                                                                                                                  ggacggTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAat           >  2:487956/1‑150 (MQ=255)
                                                                                                                                   gacggTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAatat         >  2:219849/1‑151 (MQ=255)
                                                                                                                                     cggTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATaa       <  1:298405/151‑1 (MQ=255)
                                                                                                                                       gTAACTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATAAat     <  1:188429/151‑1 (MQ=255)
                                                                                                                                         aaCTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATAAata    <  1:467030/150‑1 (MQ=255)
                                                                                                                                          aCTGACCTGTTGCAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATAAATAtt  <  2:306219/151‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                           
GTTTGTTACCGAGATCGCCGATTAATTCAGAAAGCGTACCAACCGGGCATAACCATGAGCAAAAGGCCTTTTTGAGTAATAGACTGATGACGATAAAAGCGACCAATAACAGCATCGCGGCGGCGTGGACGGACGGTAACTGACCTGTTACAAGGCTATATTTCAGATTCATCAGCCCGGCAATCGGTAGCCAGCCTTCGATACCTCCCGGTCTGGCGACAAATGTCGTGCTACTTGCCGTTTCGTAATAGCGCACCCAATACCAGAACGTGATGGCAATATAAATATT  >  NC_000913/1052948‑1053236

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A